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1 import math
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2 import re
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3 import sys
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4 import csv
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5 import pickle
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6 import lxml.etree as ET
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7
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8 from enum import Enum
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9 from itertools import count
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10 from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar, Union
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11
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12 import pandas as pd
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13 import cobra
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14
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15 # FILES
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16 class FileFormat(Enum):
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17 """
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18 Encodes possible file extensions to conditionally save data in a different format.
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19 """
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20 DAT = ("dat",) # this is how galaxy treats all your files!
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21 CSV = ("csv",) # this is how most editable input data is written
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22 TSV = ("tsv",) # this is how most editable input data is ACTUALLY written TODO:more support pls!!
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23
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24 SVG = ("svg",) # this is how most metabolic maps are written
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25 PNG = ("png",) # this is a common output format for images (such as metabolic maps)
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26 PDF = ("pdf",) # this is also a common output format for images, as it's required in publications.
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27
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28 XML = ("xml",) # this is one main way cobra models appear in
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29 JSON = ("json",) # this is the other
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30
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31 PICKLE = ("pickle", "pk", "p") # this is how all runtime data structures are saved
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32 #TODO: we're in a pickle (ba dum tss), there's no point in supporting many extensions internally. The
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33 # issue will never be solved for user-uploaded files and those are saved as .dat by galaxy anyway so it
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34 # doesn't matter as long as we CAN recognize these 3 names as valid pickle extensions. We must however
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35 # agree on an internal standard and use only that one, otherwise constructing usable paths becomes a nightmare.
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36 @classmethod
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37 def fromExt(cls, ext :str) -> "FileFormat":
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38 """
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39 Converts a file extension string to a FileFormat instance.
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40
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41 Args:
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42 ext : The file extension as a string.
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43
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44 Returns:
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45 FileFormat: The FileFormat instance corresponding to the file extension.
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46 """
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47 variantName = ext.upper()
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48 if variantName in FileFormat.__members__: return FileFormat[variantName]
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49
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50 variantName = variantName.lower()
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51 for member in cls:
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52 if variantName in member.value: return member
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53
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54 raise ValueErr("ext", "a valid FileFormat file extension", ext)
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55
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56 def __str__(self) -> str:
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57 """
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58 (Private) converts to str representation. Good practice for usage with argparse.
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59
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60 Returns:
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61 str : the string representation of the file extension.
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62 """
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63 return self.value[-1] #TODO: fix, it's the dumb pickle thing
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64
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65 class FilePath():
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66 """
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67 Represents a file path. View this as an attempt to standardize file-related operations by expecting
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68 values of this type in any process requesting a file path.
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69 """
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70 def __init__(self, filePath :str, ext :FileFormat, *, prefix = "") -> None:
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71 """
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72 (Private) Initializes an instance of FilePath.
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73
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74 Args:
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75 path : the end of the path, containing the file name.
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76 ext : the file's extension.
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77 prefix : anything before path, if the last '/' isn't there it's added by the code.
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78
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79 Returns:
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80 None : practically, a FilePath instance.
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81 """
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82 self.ext = ext
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83 self.filePath = filePath
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84
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85 if prefix and prefix[-1] != '/': prefix += '/'
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86 self.prefix = prefix
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87
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88 @classmethod
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89 def fromStrPath(cls, path :str) -> "FilePath":
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90 """
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91 Factory method to parse a string from which to obtain, if possible, a valid FilePath instance.
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92
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93 Args:
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94 path : the string containing the path
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95
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96 Raises:
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97 PathErr : if the provided string doesn't represent a valid path.
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98
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99 Returns:
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100 FilePath : the constructed instance.
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101 """
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102 # This method is often used to construct FilePath instances from ARGS UI arguments. These arguments *should*
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103 # always be correct paths and could be used as raw strings, however most if not all functions that work with
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104 # file paths request the FilePath objects specifically, which is a very good thing in any case other than this.
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105 # What ends up happening is we spend time parsing a string into a FilePath so that the function accepts it, only
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106 # to call show() immediately to bring back the string and open the file it points to.
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107 # TODO: this is an indication that the arguments SHOULD BE OF TYPE FilePath if they are filepaths, this ENSURES
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108 # their correctness when modifying the UI and avoids the pointless back-and-forth.
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109 result = re.search(r"^(?P<prefix>.*\/)?(?P<name>.*)\.(?P<ext>[^.]*)$", path)
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110 if not result or not result["name"] or not result["ext"]:
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111 raise PathErr(path, "cannot recognize folder structure or extension in path")
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112
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113 prefix = result["prefix"] if result["prefix"] else ""
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114 return cls(result["name"], FileFormat.fromExt(result["ext"]), prefix = prefix)
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115
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116 def show(self) -> str:
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117 """
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118 Shows the path as a string.
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119
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120 Returns:
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121 str : the path shown as a string.
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122 """
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123 return f"{self.prefix}{self.filePath}.{self.ext}"
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124
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125 def __str__(self) -> str: return self.show()
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126
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127 # ERRORS
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128 def terminate(msg :str) -> None:
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129 """
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130 Terminate the execution of the script with an error message.
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131
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132 Args:
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133 msg (str): The error message to be displayed.
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134
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135 Returns:
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136 None
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137 """
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138 sys.exit(f"Execution aborted: {msg}\n")
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139
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140 def logWarning(msg :str, loggerPath :str) -> None:
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141 """
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142 Log a warning message to an output log file and print it to the console. The final period and a
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143 newline is added by the function.
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144
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145 Args:
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146 s (str): The warning message to be logged and printed.
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147 loggerPath : The file path of the output log file. Given as a string, parsed to a FilePath and
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148 immediately read back (beware relative expensive operation, log with caution).
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149
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150 Returns:
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151 None
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152 """
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153 # building the path and then reading it immediately seems useless, but it's actually a way of
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154 # validating that reduces repetition on the caller's side. Besides, logging a message by writing
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155 # to a file is supposed to be computationally expensive anyway, so this is also a good deterrent from
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156 # mindlessly logging whenever something comes up, log at the very end and tell the user everything
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157 # that went wrong. If you don't like it: implement a persistent runtime buffer that gets dumped to
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158 # the file only at the end of the program's execution.
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159 with open(FilePath.fromStrPath(loggerPath).show(), 'a') as log: log.write(f"{msg}.\n")
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160
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161 class CustomErr(Exception):
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162 """
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163 Custom error class to handle exceptions in a structured way, with a unique identifier and a message.
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164 """
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165 __idGenerator = count()
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166 errName = "Custom Error"
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167 def __init__(self, msg :str, details = "", explicitErrCode = -1) -> None:
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168 """
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169 (Private) Initializes an instance of CustomErr.
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170
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171 Args:
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172 msg (str): Error message to be displayed.
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173 details (str): Informs the user more about the error encountered. Defaults to "".
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174 explicitErrCode (int): Explicit error code to be used. Defaults to -1.
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175
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176 Returns:
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177 None : practically, a CustomErr instance.
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178 """
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179 self.msg = msg
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180 self.details = details
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181
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182 self.id = max(explicitErrCode, next(CustomErr.__idGenerator))
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183
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184 def throw(self, loggerPath = "") -> None:
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185 """
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186 Raises the current CustomErr instance, logging a warning message before doing so.
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187
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188 Raises:
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189 self: The current CustomErr instance.
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190
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191 Returns:
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192 None
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193 """
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194 if loggerPath: logWarning(str(self), loggerPath)
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195 raise self
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196
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197 def abort(self) -> None:
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198 """
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199 Aborts the execution of the script.
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200
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201 Returns:
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202 None
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203 """
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204 terminate(str(self))
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205
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206 def __str__(self) -> str:
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207 """
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208 (Private) Returns a string representing the current CustomErr instance.
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209
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210 Returns:
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211 str: A string representing the current CustomErr instance.
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212 """
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213 return f"{CustomErr.errName} #{self.id}: {self.msg}, {self.details}."
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214
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215 class ArgsErr(CustomErr):
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216 """
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217 CustomErr subclass for UI arguments errors.
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218 """
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219 errName = "Args Error"
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220 def __init__(self, argName :str, expected :Any, actual :Any, msg = "no further details provided") -> None:
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221 super().__init__(f"argument \"{argName}\" expected {expected} but got {actual}", msg)
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222
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223 class DataErr(CustomErr):
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224 """
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225 CustomErr subclass for data formatting errors.
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226 """
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227 errName = "Data Format Error"
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228 def __init__(self, fileName :str, msg = "no further details provided") -> None:
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229 super().__init__(f"file \"{fileName}\" contains malformed data", msg)
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230
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231 class PathErr(CustomErr):
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232 """
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233 CustomErr subclass for filepath formatting errors.
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234 """
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235 errName = "Path Error"
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236 def __init__(self, path :FilePath, msg = "no further details provided") -> None:
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237 super().__init__(f"path \"{path}\" is invalid", msg)
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238
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239 class ValueErr(CustomErr):
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240 """
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241 CustomErr subclass for any value error.
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242 """
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243 errName = "Value Error"
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244 def __init__(self, valueName: str, expected :Any, actual :Any, msg = "no further details provided") -> None:
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245 super().__init__("value " + f"\"{valueName}\" " * bool(valueName) + f"was supposed to be {expected}, but got {actual} instead", msg)
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246
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247 # RESULT
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248 T = TypeVar('T')
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249 E = TypeVar('E', bound = CustomErr) # should bind to Result.ResultErr but python happened!
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250 class Result(Generic[T, E]):
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251 class ResultErr(CustomErr):
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252 """
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253 CustomErr subclass for all Result errors.
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254 """
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255 errName = "Result Error"
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256 def __init__(self, msg = "no further details provided") -> None:
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257 super().__init__(msg)
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258 """
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259 Class to handle the result of an operation, with a value and a boolean flag to indicate
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260 whether the operation was successful or not.
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261 """
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262 def __init__(self, value :Union[T, E], isOk :bool) -> None:
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263 """
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264 (Private) Initializes an instance of Result.
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265
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266 Args:
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267 value (Union[T, E]): The value to be stored in the Result instance.
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268 isOk (bool): A boolean flag to indicate whether the operation was successful or not.
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269
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270 Returns:
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271 None : practically, a Result instance.
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272 """
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273 self.isOk = isOk
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274 self.isErr = not isOk
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275 self.value = value
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276
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277 @classmethod
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278 def Ok(cls, value :T) -> "Result":
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279 """
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280 Constructs a new Result instance with a successful operation.
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281
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282 Args:
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283 value (T): The value to be stored in the Result instance, set as successful.
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284
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285 Returns:
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286 Result: A new Result instance with a successful operation.
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287 """
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288 return Result(value, isOk = True)
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289
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290 @classmethod
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291 def Err(cls, value :E) -> "Result":
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292 """
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293 Constructs a new Result instance with a failed operation.
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294
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295 Args:
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296 value (E): The value to be stored in the Result instance, set as failed.
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297
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298 Returns:
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299 Result: A new Result instance with a failed operation.
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300 """
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301 return Result(value, isOk = False)
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302
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303 def unwrap(self) -> T:
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304 """
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305 Unwraps the value of the Result instance, if the operation was successful.
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306
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307 Raises:
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308 ResultErr: If the operation was not successful.
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309
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310 Returns:
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311 T: The value of the Result instance, if the operation was successful.
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312 """
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313 if self.isOk: return self.value
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314 raise Result.ResultErr(f"Unwrapped Result.Err : {self.value}")
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315
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316 def unwrapOr(self, default :T) -> T:
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317 """
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318 Unwraps the value of the Result instance, if the operation was successful, otherwise
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319 it returns a default value.
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320
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321 Args:
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322 default (T): The default value to be returned if the operation was not successful.
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323
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324 Returns:
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325 T: The value of the Result instance, if the operation was successful,
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326 otherwise the default value.
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327 """
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328 return self.value if self.isOk else default
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329
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330 def expect(self, err :"Result.ResultErr") -> T:
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331 """
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332 Expects that the value of the Result instance is successful, otherwise it raises an error.
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333
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334 Args:
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335 err (Exception): The error to be raised if the operation was not successful.
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336
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337 Raises:
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338 err: The error raised if the operation was not successful.
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339
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340 Returns:
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341 T: The value of the Result instance, if the operation was successful.
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342 """
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343 if self.isOk: return self.value
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344 raise err
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345
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346 U = TypeVar("U")
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347 def map(self, mapper: Callable[[T], U]) -> "Result[U, E]":
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348 """
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349 Maps the value of the current Result to whatever is returned by the mapper function.
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350 If the Result contained an unsuccessful operation to begin with it remains unchanged
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351 (a reference to the current instance is returned).
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352 If the mapper function panics the returned result instance will be of the error kind.
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353
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354 Args:
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355 mapper (Callable[[T], U]): The mapper operation to be applied to the Result value.
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356
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357 Returns:
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358 Result[U, E]: The result of the mapper operation applied to the Result value.
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359 """
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360 if self.isErr: return self
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361 try: return Result.Ok(mapper(self.value))
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362 except Exception as e: return Result.Err(e)
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363
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364 D = TypeVar("D", bound = "Result.ResultErr")
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365 def mapErr(self, mapper :Callable[[E], D]) -> "Result[T, D]":
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366 """
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367 Maps the error of the current Result to whatever is returned by the mapper function.
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368 If the Result contained a successful operation it remains unchanged
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369 (a reference to the current instance is returned).
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370 If the mapper function panics this method does as well.
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371
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372 Args:
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373 mapper (Callable[[E], D]): The mapper operation to be applied to the Result error.
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374
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375 Returns:
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376 Result[U, E]: The result of the mapper operation applied to the Result error.
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377 """
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378 if self.isOk: return self
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379 return Result.Err(mapper(self.value))
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380
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381 def __str__(self):
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382 return f"Result::{'Ok' if self.isOk else 'Err'}({self.value})"
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383
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384 # FILES
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385 def read_dataset(path :FilePath, datasetName = "Dataset (not actual file name!)") -> pd.DataFrame:
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386 """
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387 Reads a .csv or .tsv file and returns it as a Pandas DataFrame.
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388
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389 Args:
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390 path : the path to the dataset file.
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391 datasetName : the name of the dataset.
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392
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393 Raises:
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394 DataErr: If anything goes wrong when trying to open the file, if pandas thinks the dataset is empty or if
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395 it has less than 2 columns.
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396
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397 Returns:
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398 pandas.DataFrame: The dataset loaded as a Pandas DataFrame.
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399 """
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400 # I advise against the use of this function. This is an attempt at standardizing bad legacy code rather than
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401 # removing / replacing it to avoid introducing as many bugs as possible in the tools still relying on this code.
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402 # First off, this is not the best way to distinguish between .csv and .tsv files and Galaxy itself makes it really
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403 # hard to implement anything better. Also, this function's name advertizes it as a dataset-specific operation and
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404 # contains dubious responsibility (how many columns..) while being a file-opening function instead. My suggestion is
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405 # TODO: stop using dataframes ever at all in anything and find a way to have tight control over file extensions.
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406 try: dataset = pd.read_csv(path.show(), sep = '\t', header = None, engine = "python")
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407 except:
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408 try: dataset = pd.read_csv(path.show(), sep = ',', header = 0, engine = "python")
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409 except Exception as err: raise DataErr(datasetName, f"encountered empty or wrongly formatted data: {err}")
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410
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411 if len(dataset.columns) < 2: raise DataErr(datasetName, "a dataset is always meant to have at least 2 columns")
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412 return dataset
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413
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414 def readPickle(path :FilePath) -> Any:
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415 """
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416 Reads the contents of a .pickle file, which needs to exist at the given path.
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417
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418 Args:
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419 path : the path to the .pickle file.
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420
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421 Returns:
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422 Any : the data inside a pickle file, could be anything.
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423 """
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424 with open(path.show(), "rb") as fd: return pickle.load(fd)
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425
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426 def writePickle(path :FilePath, data :Any) -> None:
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427 """
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428 Saves any data in a .pickle file, created at the given path.
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429
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430 Args:
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431 path : the path to the .pickle file.
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432 data : the data to be written to the file.
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433
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434 Returns:
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435 None
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436 """
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437 with open(path.show(), "wb") as fd: pickle.dump(data, fd)
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438
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439 def readCsv(path :FilePath, delimiter = ',', *, skipHeader = True) -> List[List[str]]:
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440 """
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441 Reads the contents of a .csv file, which needs to exist at the given path.
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442
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443 Args:
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444 path : the path to the .csv file.
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445 delimiter : allows other subformats such as .tsv to be opened by the same method (\\t delimiter).
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446 skipHeader : whether the first row of the file is a header and should be skipped.
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447
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448 Returns:
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449 List[List[str]] : list of rows from the file, each parsed as a list of strings originally separated by commas.
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450 """
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451 with open(path.show(), "r", newline = "") as fd: return list(csv.reader(fd, delimiter = delimiter))[skipHeader:]
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452
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453 def readSvg(path :FilePath, customErr :Optional[Exception] = None) -> ET.ElementTree:
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454 """
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455 Reads the contents of a .svg file, which needs to exist at the given path.
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456
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457 Args:
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458 path : the path to the .svg file.
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459
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460 Raises:
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461 DataErr : if the map is malformed.
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462
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463 Returns:
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464 Any : the data inside a svg file, could be anything.
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465 """
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466 try: return ET.parse(path.show())
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467 except (ET.XMLSyntaxError, ET.XMLSchemaParseError) as err:
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468 raise customErr if customErr else err
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469
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470 def writeSvg(path :FilePath, data:ET.ElementTree) -> None:
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471 """
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472 Saves svg data opened with lxml.etree in a .svg file, created at the given path.
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473
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474 Args:
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475 path : the path to the .svg file.
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476 data : the data to be written to the file.
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|
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477
|
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478 Returns:
|
|
|
479 None
|
|
|
480 """
|
|
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481 with open(path.show(), "wb") as fd: fd.write(ET.tostring(data))
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482
|
|
|
483 # UI ARGUMENTS
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484 class Bool:
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485 def __init__(self, argName :str) -> None:
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486 self.argName = argName
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487
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|
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488 def __call__(self, s :str) -> bool: return self.check(s)
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489
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|
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490 def check(self, s :str) -> bool:
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491 s = s.lower()
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|
|
492 if s == "true" : return True
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|
|
493 if s == "false": return False
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|
|
494 raise ArgsErr(self.argName, "boolean string (true or false, not case sensitive)", f"\"{s}\"")
|
|
|
495
|
|
|
496 class Float:
|
|
|
497 def __init__(self, argName = "Dataset values, not an argument") -> None:
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|
|
498 self.argName = argName
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|
|
499
|
|
|
500 def __call__(self, s :str) -> float: return self.check(s)
|
|
|
501
|
|
|
502 def check(self, s :str) -> float:
|
|
|
503 try: return float(s)
|
|
|
504 except ValueError:
|
|
|
505 s = s.lower()
|
|
|
506 if s == "nan" or s == "none": return math.nan
|
|
|
507 raise ArgsErr(self.argName, "numeric string or \"None\" or \"NaN\" (not case sensitive)", f"\"{s}\"")
|
|
|
508
|
|
|
509 # MODELS
|
|
|
510 OldRule = List[Union[str, "OldRule"]]
|
|
|
511 class Model(Enum):
|
|
|
512 """
|
|
|
513 Represents a metabolic model, either custom or locally supported. Custom models don't point
|
|
|
514 to valid file paths.
|
|
|
515 """
|
|
|
516
|
|
|
517 Recon = "Recon"
|
|
|
518 ENGRO2 = "ENGRO2"
|
|
|
519 ENGRO2_no_legend = "ENGRO2_no_legend"
|
|
|
520 HMRcore = "HMRcore"
|
|
|
521 HMRcore_no_legend = "HMRcore_no_legend"
|
|
|
522 Custom = "Custom" # Exists as a valid variant in the UI, but doesn't point to valid file paths.
|
|
|
523
|
|
|
524 def __raiseMissingPathErr(self, path :Optional[FilePath]) -> None:
|
|
|
525 if not path: raise PathErr("<<MISSING>>", "it's necessary to provide a custom path when retrieving files from a custom model")
|
|
|
526
|
|
|
527 def getRules(self, toolDir :str, customPath :Optional[FilePath] = None) -> Dict[str, Dict[str, OldRule]]:
|
|
|
528 """
|
|
|
529 Open "rules" file for this model.
|
|
|
530
|
|
|
531 Returns:
|
|
|
532 Dict[str, Dict[str, OldRule]] : the rules for this model.
|
|
|
533 """
|
|
|
534 path = customPath if self is Model.Custom else FilePath(f"{self.name}_rules", FileFormat.PICKLE, prefix = f"{toolDir}/local/pickle files/")
|
|
|
535 self.__raiseMissingPathErr(path)
|
|
|
536 return readPickle(path)
|
|
|
537
|
|
|
538 def getTranslator(self, toolDir :str, customPath :Optional[FilePath] = None) -> Dict[str, Dict[str, str]]:
|
|
|
539 """
|
|
|
540 Open "gene translator (old: gene_in_rule)" file for this model.
|
|
|
541
|
|
|
542 Returns:
|
|
|
543 Dict[str, Dict[str, str]] : the translator dict for this model.
|
|
|
544 """
|
|
|
545 path = customPath if self is Model.Custom else FilePath(f"{self.name}_genes", FileFormat.PICKLE, prefix = f"{toolDir}/local/pickle files/")
|
|
|
546 self.__raiseMissingPathErr(path)
|
|
|
547 return readPickle(path)
|
|
|
548
|
|
|
549 def getMap(self, toolDir = ".", customPath :Optional[FilePath] = None) -> ET.ElementTree:
|
|
|
550 path = customPath if self is Model.Custom else FilePath(f"{self.name}_map", FileFormat.SVG, prefix = f"{toolDir}/local/svg metabolic maps/")
|
|
|
551 self.__raiseMissingPathErr(path)
|
|
|
552 return readSvg(path, customErr = DataErr(path, f"custom map in wrong format"))
|
|
|
553
|
|
|
554 def getCOBRAmodel(self, toolDir = ".", customPath :Optional[FilePath] = None, customExtension :Optional[FilePath]=None)->cobra.Model:
|
|
|
555 if(self is Model.Custom):
|
|
|
556 return self.load_custom_model(customPath, customExtension)
|
|
|
557 else:
|
|
|
558 return cobra.io.read_sbml_model(FilePath(f"{self.name}", FileFormat.XML, prefix = f"{toolDir}/local/models/").show())
|
|
|
559
|
|
|
560 def load_custom_model(self, file_path :FilePath, ext :Optional[FileFormat] = None) -> cobra.Model:
|
|
|
561 ext = ext if ext else file_path.ext
|
|
|
562 try:
|
|
|
563 if ext is FileFormat.XML:
|
|
|
564 return cobra.io.read_sbml_model(file_path.show())
|
|
|
565
|
|
|
566 if ext is FileFormat.JSON:
|
|
|
567 return cobra.io.load_json_model(file_path.show())
|
|
|
568
|
|
|
569 except Exception as e: raise DataErr(file_path, e.__str__())
|
|
|
570 raise DataErr(file_path,
|
|
|
571 f"Fomat \"{file_path.ext}\" is not recognized, only JSON and XML files are supported.")
|
|
|
572
|
|
|
573 def __str__(self) -> str: return self.value |
